BioDiVinE: A Framework for Parallel Analysis of Biological Models

• Authors: BARNAT Jiří; BRIM Luboš; ČERNÁ Ivana; DRAŽAN Sven; FABRIKOVÁ Jana; LÁNÍK Jan; ŠAFRÁNEK David; HONGWU Ma
• Year of publication: 2009
• Type: Article in Proceedings
• Conference: Proceedings of 2nd International Workshop on Computational Models for Cell Processes
• MU Faculty or unit: Faculty of Informatics
• Field: Informatics
• Keywords: model checking; multi-affine systems; dynamic systems; rectangular abstraction
• Description: In this paper a novel tool BioDiVinE for parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study.

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